In order to characterize a side-reaction in Fmoc based solid-phase synthesis, a stepwise detection method has been carried out. The resulting peptides have been subjected to analyze through HPLC, electrospray mass spectrometry and laser desorption mass spectrometry. By comparison of the results from individual peptides, we have been able to define that the problem in the synthesis was due to aspartimide formation followed by a piperidine addition to the peptide. A number of pentapeptides based on Fmoc approach have been made for testing those residues reported susceptible in Boc chemistry. Further, we are seeking an efficient method to minimize this side-reaction in Fmoc based solid phase synthesis. All of the above work requires analytical methods including MS to elucidate the side reaction products. A paper describing this work has been published.